Several classes of antibiotics have been designed to target gram-negative bacteria, including aminopenicillins, ureidopenicillins, cephalosporins, beta-lactam-betalactamase combinations (e.g. pipercillin-tazobactam), Folate antagonists, quinolones, and carbapenems. Many of these antibiotics also cover gram positive organisms. The drugs that specifically target gram negative organisms include aminoglycosides, monobactams (aztreonam) and Ciprofloxacin.

Along with cell shape, gram-staining is a rapid diagnostic tool and once was used to group species at the subdivision of Bacteria.
Historically, the kingdom Monera was divided into four divisions based on gram-staining: Firmacutes (+), Gracillicutes (−), Mollicutes (0) and Mendocutes (var.).[3]
Since 1987, the monophyly of the gram-negative bacteria has been disproven with molecular studies.[4] However some authors, such as Cavalier-Smith still treat them as a monophyletic taxon (though not a clade; his definition of monophyly requires a single common ancestor but does not require holophyly, the property that all descendants be encompassed by the taxon) and refer to the group as a subkingdom "Negibacteria".[5]

Bacteria are traditionally classified based on their gram-staining response into the gram-positive (or monoderm, "one membrane") and gram-negative (diderm, "two membranes") groups. It was traditionally thought that the groups represent lineages, i.e. the extra membrane only evoved once, such that gram-negative bacteria are more closely related to one another than to any gram-positive bacteria. While this is often true, the classification system breaks down in some cases, with lineage groupings not matching the staining result.[6][7][8][9] Thus, gram-staining cannot be reliably used to assess familial relationships of bacteria. Nevertheless, staining often gives reliable information about the composition of the cell membrane, distinguishing between the presence or absence of an outer lipid membrane.[6][10]

Of these two structurally distinct groups of prokaryotic organisms, monoderm prokaryotes are thought to be ancestral. Based upon a number of different observations including that the gram-positive bacteria are the major reactors to antibiotics and that gram-negative bacteria are, in general, resistant to them, it has been proposed that the outer cell membrane in gram-negative bacteria (diderms) evolved as a protective mechanism against antibiotic selection pressure.[6][7][10][11] Some bacteria such as Deinococcus, which stain gram-positive due to the presence of a thick peptidoglycan layer, but also possess an outer cell membrane are suggested as intermediates in the transition between monoderm (gram-positive) and diderm (gram-negative) bacteria.[6][11] The diderm bacteria can also be further differentiated between simple diderms lacking lipopolysaccharide (LPS); the archetypical diderm bacteria, in which the outer cell membrane contains lipopolysaccharide; and the diderm bacteria, in which the outer cell membrane is made up of mycolic acid (e. g. Mycobacterium).[8][9][11][12]

Transformation is one of three processes for horizontal gene transfer, in which exogenous genetic material passes from bacterium to another, the other two being conjugation (transfer of genetic material between two bacterial cells in direct contact) and transduction (injection of foreign DNA by a bacteriophage virus into the host bacterium).[13] In transformation, the genetic material passes through the intervening medium, and uptake is completely dependent on the recipient bacterium.[13]

One of the several unique characteristics of gram-negative bacteria is the structure of the bacterial outer membrane. The outer leaflet of this membrane comprises a complex lipopolysaccharide (LPS) whose lipid portion acts as an endotoxin. If gram-negative bacteria enter the circulatory system, the liposaccharide can cause a toxic reaction. This results in fever, an increased respiratory rate, and low blood pressure. This may lead to life-threatening septic shock.[2]

The outer membrane protects the bacteria from several antibiotics, dyes, and detergents that would normally damage either the inner membrane or the cell wall (made of peptidoglycan). The outer membrane provides these bacteria with resistance to lysozyme and penicillin. The periplasmic space (space between the two cell membranes) also contains enzymes which break down or modify antibiotics. Drugs commonly used to treat gram negative infections include amino, carboxy and ureido penicillins (ampicillin, amoxicillin, pipercillin, ticarcillin) these drugs may be combined with beta-lactamase inhibitors to combat the presence of enzymes that can digest these drugs (known as beta-lactamases) in the peri-plasmic space. Other classes of drugs that have gram negative spectrum include cephalosporins, monobactams (aztreonam), aminogylosides, quinolones, macrolides, chloramphenicol, folate antagonists, and carbapenems.[15]

The pathogenic capability of gram-negative bacteria is often associated with certain components of their membrane, in particular, the LPS.[1] In humans, the presence of LPS triggers an innate immune response, activating the immune system and producing cytokines (hormonal regulators). Inflammation is a common reaction to cytokine production, which can also produce host toxicity. The innate immune response to LPS, however, is not synonymous with pathogenicity, or the ability to cause disease.[citation needed]